Waterborne norovirus outbreak in a municipal drinking-water supply in Sweden.

During Easter 2009, almost 200 people resident in a small Swedish village fell ill with gastrointestinal symptoms. We conducted a retrospective cohort study and a molecular investigation in order to identify the source of the outbreak. Residents living in households connected to the public water network were at an increased risk of developing disease (relative risk 4·80, 95% confidence interval 1·68-13·73) compared to those with no connection to the public network. Norovirus genotype GI.3 was identified in stool samples from six patients and in a sample from the public water network. Contamination of one of the wells supplying the public water network was thought to be the source of the outbreak. This is a description of a norovirus outbreak linked to a municipal drinking-water supply in Sweden. Information from epidemiological and molecular investigations is of utmost importance to guide outbreak control measures and to prevent future outbreaks.

Cross-sectional survey of health management and prevalence of vector-borne diseases, endoparasites and ectoparasites in Samoan dogs.

OBJECTIVE: To determine the prevalence of selected canine vector-borne diseases (Leishmania infantum, Anaplasma spp., Ehrlichia canis, Borrelia burgdorferi and Dirofilaria immitis) and endo- and ectoparasites in Samoan dogs presenting for surgical sterilisation and to report on the general health management of the dogs. METHODS: This study was a prospective serological cross-sectional survey. Management data were obtained for 242 dogs by interview with their owners. Blood samples were collected from 237 dogs and screened for the canine vector-borne diseases using point-of-care qualitative ELISA assays. Anaplasma spp. positive samples were screened by PCR and sequenced for species identification. Rectal faecal samples were collected from 204 dogs for faecal flotation and immunofluorescent antibody tests were performed for Giardia and Cryptosporidium spp. on a subset of 93 faecal samples. The skin and coat of 221 dogs were examined for presence of ectoparasites. RESULTS: The D. immitis antigen was detected in 46.8% (111/237) of dogs. Seroprevalence of Anaplasma spp. was 8.4% (20/237); A. platys was confirmed by PCR. Prevalence of hookworm was 92.6% (185/205) and Giardia was 29.0% (27/93). Ectoparasites were detected on 210/221 (95.0%) of dogs examined and 228/242 dogs (94.2%) had previously never received any preventative medication. CONCLUSIONS: There was a very high prevalence of D. immitis, hookworm and external parasites in Samoan dogs, and prophylactic medication is rarely administered. This is the first report confirming A. platys in Samoa and the South Pacific islands. The public health implications of poor management of the dogs should be considered and investigated further.

Hidden Markov models in computational biology. Applications to protein modeling.

Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated on the globin family, the protein kinase catalytic domain, and the EF-hand calcium binding motif. In each case the parameters of an HMM are estimated from a training set of unaligned sequences. After the HMM is built, it is used to obtain a multiple alignment of all the training sequences. It is also used to search the SWISS-PROT 22 database for other sequences that are members of the given protein family, or contain the given domain. The HMM produces multiple alignments of good quality that agree closely with the alignments produced by programs that incorporate three-dimensional structural information. When employed in discrimination tests (by examining how closely the sequences in a database fit the globin, kinase and EF-hand HMMs), the HMM is able to distinguish members of these families from non-members with a high degree of accuracy. Both the HMM and PROFILESEARCH (a technique used to search for relationships between a protein sequence and multiply aligned sequences) perform better in these tests than PROSITE (a dictionary of sites and patterns in proteins). The HMM appears to have a slight advantage over PROFILESEARCH in terms of lower rates of false negatives and false positives, even though the HMM is trained using only unaligned sequences, whereas PROFILESEARCH requires aligned training sequences. Our results suggest the presence of an EF-hand calcium binding motif in a highly conserved and evolutionary preserved putative intracellular region of 155 residues in the alpha-1 subunit of L-type calcium channels which play an important role in excitation-contraction coupling. This region has been suggested to contain the functional domains that are typical or essential for all L-type calcium channels regardless of whether they couple to ryanodine receptors, conduct ions or both.

Characterization of Tula virus antigenic determinants defined by monoclonal antibodies raised against baculovirus-expressed nucleocapsid protein.

Tula virus was recently discovered by RT-PCR in lung samples from European common voles (Microtus arvalis and M. rossiaemeridionalis). Since virus isolation attempts had been unsuccessful, no antigen was available for analysis or for use in immunoassays. To circumvent this, complete Tula virus nucleocapsid protein (bac-TUL-N) was expressed in recombinant baculovirus. Rodent antibody end-point titers to bac-TUL-N and to truncated N fragments indicated that the NH2-terminal region is the major antigenic target and revealed a high cross-reactivity to Puumala virus N. Immunizations with crude bac-TUL-N preparations evoked high antibody responses to native hantavirus N in Balb/c mice and six monoclonal antibodies (Mabs) were generated. Epitope mapping of the Mabs, based on a competitive assay, reactivities to truncated recombinant N fragments, and reactivity patterns to different hantavirus strains, identified five recognition sites on Tula virus N. One epitope, which was identified as specific for Tula virus, was located in a region of N which is highly variable among the hantaviruses (aa 226-293), and four epitopes were mapped to the NH2-terminal region of the protein (aa 1-61). One epitope was expressed only in Tula and Prospect Hill viruses, one epitope in Tula, Prospect Hill, Khabarovsk, and Sin Nombre viruses, while two epitopes were conserved in all examined hantaviruses carried by rodents within the subfamily Arvicolinae of the Muridae family.

Dobrava virus infection: serological diagnosis and cross-reactions to other hantaviruses.

Recent data have shown that Dobrava (DOB) hantavirus is the cause of severe haemorrhagic fever with renal syndrome (HFRS) in central and eastern Europe. To determine whether serological assays need to be based on the homologous viral antigen rather than on closely related hantavirus antigens, acute and convalescent sera from patients with HFRS collected in former Yugoslavia were examined for IgM and IgG to three hantavirus antigens; DOB, Hantaan (HTN) and Puumala (PUU). Focus reduction neutralization test was included for comparison and confirmation of the enzyme-linked immunosorbent assay (ELISA) results. Although the results showed that the cross-reactivity was high between these three antigens during the acute phase of the disease, one of 155 patients serum samples reacted only in the DOB antigen-based IgM assay. The evaluation of IgG reactivities revealed that a DOB antigen-based IgG ELISA has to be used in sero-epidemiological studies; 7.1% (11/155) of the acute phase/early convalescent sera and 12.5% (2/16) of the late convalescent sera, respectively, reacted only with the homologous DOB antigen.

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.

UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the 'Dicty annotation marathon', a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations.

Phylogenetic inference in protein superfamilies: analysis of SH2 domains.

This work focuses on the inference of evolutionary relationships in protein superfamilies, and the uses of these relationships to identify key positions in the structure, to infer attributes on the basis of evolutionary distance, and to identify potential errors in sequence annotations. Relative entropy, a distance metric from information theory, is used in combination with Dirichlet mixture priors to estimate a phylogenetic tree for a set of proteins. This method infers key structural or functional positions in the molecule, and guides the tree topology to preserve these important positions within subtrees. Minimum-description-length principles are used to determine a cut of the tree into subtrees, to identify the subfamilies in the data. This method is demonstrated on SH2-domain containing proteins, resulting in a new subfamily assignment for Src2-drome and a suggested evolutionary relationship between Nck_human and Drk_drome, Sem5_caeel, Grb2_human and Grb2_chick.

Diagnostic potential of puumala virus nucleocapsid protein expressed in Drosophila melanogaster cells.

Puumala virus (PUU) nucleocapsid protein (N) was expressed in insect cells by using the Drosophila Expression System (DES; Invitrogen BV, Groningen, The Netherlands). Stable transfectants were established by hygromycin B selection and showed continuous expression of the recombinant protein (DES-PUU-N) for at least 5 months. The antigenic property of DES-PUU-N was shown to be identical to that of native PUU N when examined with a panel of hantavirus-specific monoclonal antibodies. Enzyme-linked immunosorbent assays (ELISAs) for detection of human immunoglobulin M (IgM) and IgG antibodies were established by using DES-PUU-N as antigen and were compared to assays based on native N. The ELISAs were evaluated for patient diagnosis and seroepidemiological purposes with panels of sera collected from patients with hemorrhagic fever with renal syndrome (HFRS) and from healthy blood donors. Equally high sensitivities and specificities for detection of PUU-specific IgM in acute-phase HFRS patient sera were obtained by the ELISA based on DES-PUU-N and the assay based on the native antigen. For detection of PUU-specific IgG, the ELISA based on monoclonal antibody-captured DES-PUU-N antigen showed optimal sensitivity and specificity.

Serological divergence of Dobrava and Saaremaa hantaviruses: evidence for two distinct serotypes.

In order to investigate the serological relationship of Dobrava hantavirus (DOBV, originating from Slovenia) and the Dobrava-like Saaremaa virus (SAAV, recently discovered in Estonia) we analysed 37 human serum samples, 24 from Estonia and 13 from the Balkans, by focus reduction neutralization test (FRNT). Most of the Estonian sera (19), including all sera from Saaremaa island (12), reacted with higher FRNT end-point titres to the local SAAV; the majority of them (15 and 11, respectively), with at least fourfold or higher titres to SAAV than to DOBV. In contrast, out of the 13 sera collected in Slovenia, Bosnia-Herzegovina and Greece, only one reacted more strongly with SAAV (with a twofold higher titre), while 10 of these sera reacted more strongly with the local DOBV (9/10 with fourfold or higher titres). These results indicate that DOBV and SAAV define unique hantavirus serotypes.

Using Dirichlet mixture priors to derive hidden Markov models for protein families.

A Bayesian method for estimating the amino acid distributions in the states of a hidden Markov model (HMM) for a protein family or the columns of a multiple alignment of that family is introduced. This method uses Dirichlet mixture densities as priors over amino acid distributions. These mixture densities are determined from examination of previously constructed HMMs or multiple alignments. It is shown that this Bayesian method can improve the quality of HMMs produced from small training sets. Specific experiments on the EF-hand motif are reported, for which these priors are shown to produce HMMs with higher likelihood on unseen data, and fewer false positives and false negatives in a database search task.

Cell culture adaptation of Puumala hantavirus changes the infectivity for its natural reservoir, Clethrionomys glareolus, and leads to accumulation of mutants with altered genomic RNA S segment.

This paper reports the establishment of a model for hantavirus host adaptation. Wild-type (wt) (bank vole-passaged) and Vero E6 cell-cultured variants of Puumala virus strain Kazan were analyzed for their virologic and genetic properties. The wt variant was well adapted for reproduction in bank voles but not in cell culture, while the Vero E6 strains replicated to much higher efficiency in cell culture but did not reproducibly infect bank voles. Comparison of the consensus sequences of the respective viral genomes revealed no differences in the coding region of the S gene. However, the noncoding regions of the S gene were found to be different at positions 26 and 1577. In one additional and independent adaptation experiment, all analyzed cDNA clones from the Vero E6-adapted variant were found to carry substitutions at position 1580 of the S segment, just 3 nucleotides downstream of the mutation observed in the first adaptation. No differences were found in the consensus sequences of the entire M segments from the wt and the Vero E6-adapted variants. The results indicated different impacts of the S and the M genomic segments for the adaptation process and selective advantages for the variants that carried altered noncoding sequences of the S segment. We conclude that the isolation in cell culture resulted in a phenotypically and genotypically altered hantavirus.

Modifying the cellular transport of DNA-based vaccines alters the immune response to hantavirus nucleocapsid protein.

Puumala virus is a member of the hantavirus genus (family Bunyaviridae) and is one of the causative agents of hemorrhagic fever with renal syndrome (HFRS) in Europe. A genetic vaccination approach was conducted to investigate if the immune response could be modulated using different cellular secretion and/or localisation signals, and the immune responses were analysed in BALB/c mice and in a bank vole infectious model. Rodents vaccinated with DNA constructs encoding the antigen fused to an amino-terminal secretion signal raised significantly higher antibody levels when compared to using constructs lacking secretion signals. Furthermore, the ratios of the IgG subclasses (IgG2a/IgG1) were raised by the use of cellular localisation signals, indicating a more pronounced Th1-type of immune response. The majority of the mice, or bank voles, immunised with DNA encoding a secreted form of the antigen showed a positive lymphoproliferative response and were protected against challenge with Puumala virus (strain Kazan-wt).

Stochastic context-free grammars for tRNA modeling.

Stochastic context-free grammars (SCFGs) are applied to the problems of folding, aligning and modeling families of tRNA sequences. SCFGs capture the sequences' common primary and secondary structure and generalize the hidden Markov models (HMMs) used in related work on protein and DNA. Results show that after having been trained on as few as 20 tRNA sequences from only two tRNA subfamilies (mitochondrial and cytoplasmic), the model can discern general tRNA from similar-length RNA sequences of other kinds, can find secondary structure of new tRNA sequences, and can produce multiple alignments of large sets of tRNA sequences. Our results suggest potential improvements in the alignments of the D- and T-domains in some mitochondrial tRNAs that cannot be fit into the canonical secondary structure.

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology.

We present a method for condensing the information in multiple alignments of proteins into a mixture of Dirichlet densities over amino acid distributions. Dirichlet mixture densities are designed to be combined with observed amino acid frequencies to form estimates of expected amino acid probabilities at each position in a profile, hidden Markov model or other statistical model. These estimates give a statistical model greater generalization capacity, so that remotely related family members can be more reliably recognized by the model. This paper corrects the previously published formula for estimating these expected probabilities, and contains complete derivations of the Dirichlet mixture formulas, methods for optimizing the mixtures to match particular databases, and suggestions for efficient implementation.

A neutralizing recombinant human antibody Fab fragment against Puumala hantavirus.

A combinatorial human antibody Fab pComb3H library, generated from splenic lymphocytes of a Puumala hantavirus (PUUV) immune individual, was selected against PUUV using the phage display technique. Panning was carried out with antigens immobilized by MAbs directed to the two PUUV envelope glycoproteins G1 and G2. Thirteen Fabs, with reactivity directed to PUUV and specifically the G2 protein, as assessed by immunofluorescence and ELISA respectively, were isolated in crude preparations. By a focus reduction neutralization test (FRNT), four of the 13 crude Fab preparations exhibited type-specific neutralization of PUUV (strain Sotkamo) with 44-54% reduction in the number of foci. After affinity purification, the four Fab clones exhibited 50% focus reduction of PUUV at concentrations below 2 microg/ml. Sequencing of the heavy and light chain complementarity determining regions (CDR) 1-3 showed that the four selected clones were identical within the antibody binding regions. In inhibition tests with the PUUV G2-specific MAbs, 4G2 and 1C9, a new epitope important for neutralization, designated as G2-a3, was defined. This epitope, overlapping partially the neutralizing epitope recognized by the human MAb 1C9, seems to be unique for the PUUV serotype since none of the Fab clones neutralized any of the other hantaviruses tested.

Predicting protein structure using hidden Markov models.

We discuss how methods based on hidden Markov models performed in the fold-recognition section of the CASP2 experiment. Hidden Markov models were built for a representative set of just over 1,000 structures from the Protein Data Bank (PDB). Each CASP2 target sequence was scored against this library of HMMs. In addition, an HMM was built for each of the target sequences and all of the sequences in PDB were scored against that target model, with a good score on both methods indicating a high probability that the target sequence is homologous to the structure. The method worked well in comparison to other methods used at CASP2 for targets of moderate difficulty, where the closest structure in PDB could be aligned to the target with at least 15% residue identity.

Isolation and characterization of Puumala hantavirus from Norway: evidence for a distinct phylogenetic sublineage.

Puumala (PUU) hantavirus is the aetiological agent of nephropathia epidemica (NE), a mild form of haemorrhagic fever with renal syndrome, which occurs in Fennoscandia, central Europe and Russia. In Norway, NE-like disease has been reported since 1946 and about 50 cases are diagnosed annually; however, the causative agent has not been characterized. In this study, a virus originating from bank voles (Clethrionomys glareolus) trapped near the town of Eidsvoll (Akershus county) was isolated and passaged in laboratory-bred bank voles. The bank vole strain was identified as a PUU virus by serological typing and by sequence analysis of the S and M gene segments. For comparison, complete or partial S sequences were determined for wild-type PUU strains from five locations in Sweden, two inhabited by the southern variant of bank vole present in Fennoscandia, and three by the northern variant. Phylogenetic analysis showed that Norwegian PUU strains are clustered together with Swedish strains from the first group forming a well-supported sublineage within the PUU genotype, distinct from other sublineages from northern Sweden, Finland, Russia and France. The results are consistent with the view of a complex evolutionary history of PUU strains in post-glacial Fennoscandia. Analyses of the current collection of nucleotide sequences suggest that PUU is the most variable genotype of the known hantaviruses.

Characterization of Puumala virus nucleocapsid protein: identification of B-cell epitopes and domains involved in protective immunity.

B-cell epitopes in the nucleocapsid protein (N) of Puumala (PUU) virus were investigated by use of truncated recombinant proteins and overlapping peptides. Six of seven epitopes, recognized by bank vole monoclonal antibodies, were localized within the amino-terminal region of the protein (aa 1-79). Polyclonal antibodies from wild-trapped or experimentally infected bank voles identified epitopes located over the entire protein. Antibody end-point titers to different N fragments indicated that the amino-terminal region is the major antigenic target in PUU virus-infected bank voles. To investigate the role of PUU virus N in protective immunity, we analyzed the immunogenicity of truncated recombinant N and developed an animal model based on colonized bank voles. No PUU virus N antigen, nor any glycoprotein-specific antibodies, could be detected after virus challenge in animals immunized with an amino-terminal fragment (aa 1-118), a fragment covering two thirds of the animals immunized with shorter N fragments displayed either N antigen, or glycoprotein-specific antibodies, suggestive of partial protection. Prechallenge sera from all groups of immunized animals were found negative or only weakly positive for neutralizing antibodies when assayed by focus reduction neutralization test, which indicated an important role for cell-mediated immunity in protection.

Rodent host specificity of European hantaviruses: evidence of Puumala virus interspecific spillover.

In order to investigate rodent host specificity of European hantaviruses, experimental infection of colonized and wild-trapped rodents was performed. In addition to the natural rodent reservoir, Clethrionomys glareolus, Puumala hantavirus (PUUV) could infect colonized Microtus agrestis and Lemmus sibiricus, but not Syrian hamsters or Balb/C mice. Neither C. glareolus, nor M. agrestis, could be readily infected by Tula hantavirus (TULV). Wild-trapped Apodemus flavicollis and A. agrarius, the natural reservoirs of Dobrava (DOBV) and Saaremaa (SAAV) hantaviruses, respectively, could both be infected by SAAV. NMRI mice could also be infected by SAAV, but with lower efficiency as compared to Apodemus mice. Balb/C and NMRI laboratory mice, but not C. glareolus, could be infected by DOBV. To our knowledge, this is the first time DOBV and SAAV have been shown to infect adult laboratory mice. Moreover, potential hantavirus spillover infections were investigated in wild-trapped rodents. In addition to the natural host C. glareolus, we also found M. arvalis and A. sylvaticus with a history of PUUV infection. We did not find any C. glareolus or A. sylvaticus infected with TULV, a hantavirus which is known to circulate in the same geographical regions of Belgium.